DISCOVERY OF PUTATIVE REGULATORY GENES BY THE MINING AND DIFFERENTIAL EXPRESSION ANALYSIS OF PINE XYLEM EST DATASETS

¹ Forest Biology Research Center, Pavillon CE Marchand, Université Laval, Québec, Québec, CANADA, G1K 7P4

² Centre de Bioinformatique de l'Université Laval, Pavillon CE Marchand, Université Laval, Québec, Québec, CANADA, G1K 7P4

Random sequencing of ESTs is a valuable approach for gene discovery in less well characterized organisms like forest trees. We are using differential expression analysis of pine EST data from six large non-normalized loblolly pine xylem cDNA libraries to identify putative gene expression clusters related to xylem formation. In our analysis, we considered ESTs belonging to 6810 Tentative Consensus sequences (TCs) in the TIGR Pinus Gene Index (PGI). EST frequencies were compared among the 800 abundantly represented TCs, by performing five different statistical tests, thus identifying 260 differentially represented gene sequences. A distance matrix between the 260 differential TCs was calculated from the correlation matrix and used to obtain a UPGMA phenogram with the PHYLIP software. Five clusters represented genes preferentially represented in one of the xylem samples (side wood, compression wood, plannings, root xylem, late wood) and, one cluster contained genes coordinately expressed in compression and side wood. Further analysis focused on the cluster sequences preferentially found in root xylem because it contained numerous non annotated sequences, i.e sequences with no known homologues or that are similar to Arabidopsis genes of unknown function. Analyses of the non annotated sequences uncovered five transcription factors: one R2R3 class MYB, two 1R class MYBs, an Arabidopsis Pleiotropic Regulatory Locus interacting protein homolog and a transcriptional activator homologue not previously reported in plants. Comprehensive sequence analysis of the remaining non annotated cDNAs of this intriguing group of genes is underway to asses their potentially role in xylem development in roots.